jbrowse-plugin-protein3d 0.8.0 → 0.8.2

package/dist/AddHighlightModel/GenomeTo1DProteinHoverHighlight.js

@@ -3,7 +3,7 @@ import { SimpleFeature, getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import Highlight from './Highlight';
 import { protein1DViewRegistry } from '../Protein1DViewRegistry';
-import { checkHovered } from '../ProteinView/util';
+import { genomeHoverToTranscriptPos } from '../ProteinView/util';
 import { genomeToTranscriptSeqMapping } from '../mappings';
 const GenomeTo1DProteinHoverHighlight = observer(function GenomeTo1DProteinHoverHighlight({ model, }) {
     const session = getSession(model);
@@ -17,17 +17,8 @@ const GenomeTo1DProteinHoverHighlight = observer(function GenomeTo1DProteinHover
     if (!protein1DInfo) {
         return null;
     }
-    if (!checkHovered(hovered)) {
-        return null;
-    }
-    const { coord, refName } = hovered.hoverPosition;
     const feature = new SimpleFeature(protein1DInfo.feature);
-    const mapping = genomeToTranscriptSeqMapping(feature);
-    const { g2p } = mapping;
-    // g2p is keyed by genomic position on the transcript's own refName; without
-    // this gate the same numeric coord on an unrelated chromosome would match a
-    // key and light a protein residue for a different locus.
-    const proteinPos = refName === mapping.refName ? g2p[coord - 1] : undefined;
+    const proteinPos = genomeHoverToTranscriptPos(hovered, genomeToTranscriptSeqMapping(feature));
     if (proteinPos === undefined) {
         return null;
     }

package/dist/AddHighlightModel/ProteinToGenomeHighlightInner.js

@@ -2,17 +2,21 @@ import React from 'react';
 import { getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import Highlight from './Highlight';
-import { getProteinView } from './util';
+import { getProteinViews, getStructuresConnectedTo } from './proteinViewLookup';
 const ProteinToGenomeHighlightInner = observer(function ProteinToGenomeHighlightInner({ model, field, }) {
     const session = getSession(model);
     const { assemblyManager } = session;
-    const { assemblyNames } = model;
-    const proteinView = getProteinView(session);
+    const { assemblyNames, id: viewId } = model;
     const assemblyName = assemblyNames[0];
     const assembly = assemblyName
         ? assemblyManager.get(assemblyName)
         : undefined;
-    return assembly && assemblyName ? (React.createElement(React.Fragment, null, proteinView?.structures.flatMap((structure, idx) => structure[field].map((r, idx2) => (React.createElement(Highlight, { key: `${r.refName}-${r.start}-${r.end}-${idx}-${idx2}`, model: model, region: {
+    // Only structures that declare this genome view as their connection: the
+    // regions are transcript coordinates on that view's assembly, so painting
+    // them into any other genome view would place a highlight at coordinates
+    // that mean nothing there.
+    const structures = getStructuresConnectedTo(getProteinViews(session), viewId);
+    return assembly && assemblyName ? (React.createElement(React.Fragment, null, structures.flatMap((structure, idx) => structure[field].map((r, idx2) => (React.createElement(Highlight, { key: `${r.refName}-${r.start}-${r.end}-${idx}-${idx2}`, model: model, region: {
             start: r.start,
             end: r.end,
             refName: r.refName,

package/dist/AddHighlightModel/ProteinToMsaHoverSync.js

@@ -4,7 +4,7 @@ import { autorun, untracked } from 'mobx';
 import { observer } from 'mobx-react';
 import { findConnectedMsaView } from './findConnectedMsaView';
 import { findStructureRowName } from './msaRowMatch';
-import { getProteinView } from './util';
+import { getProteinView } from './proteinViewLookup';
 import { stripStopCodon } from '../LaunchProteinView/utils/util';
 const ProteinToMsaHoverSync = observer(function ProteinToMsaHoverSync({ model, }) {
     const session = getSession(model);
@@ -27,7 +27,11 @@ const ProteinToMsaHoverSync = observer(function ProteinToMsaHoverSync({ model, }
         // on every hover, so the per-hover conversions below stay cheap.
         let structureRowName;
         disposers.push(autorun(() => {
-            const seq = proteinView.primaryStructure?.structureSequences?.[0];
+            // The *mapped* entity, not entity [0]: hover positions below are in the
+            // mapped entity's coordinates (molstar interactions are gated to it), so
+            // matching chain A's sequence for a heteromer whose gene is chain C
+            // finds no row and silently falls back to a wrong 1:1 mapping.
+            const seq = proteinView.primaryStructure?.mappedStructureSeq;
             structureRowName = findStructureRowName(msaView.rowMap, seq === undefined ? undefined : stripStopCodon(seq));
         }));
         if (msaView.setMousePos) {

package/dist/AddHighlightModel/proteinViewLookup.d.ts

@@ -0,0 +1,37 @@
+import type { JBrowsePluginProteinStructureModel } from '../ProteinView/model';
+import type { AbstractSessionModel } from '@jbrowse/core/util';
+/**
+ * What the highlight/hover bridges need from a ProteinView. Declared
+ * structurally (like ParentProteinView in structureModel.ts) because the MST
+ * Instance type of `structures` widens to a snapshot union at the array
+ * boundary, which would force a cast at every call site.
+ */
+export interface HighlightSourceProteinView {
+    id: string;
+    connectedMsaViewId?: string;
+    structures: JBrowsePluginProteinStructureModel[];
+    primaryStructure?: JBrowsePluginProteinStructureModel;
+}
+export declare function getProteinViews(session: AbstractSessionModel): HighlightSourceProteinView[];
+/**
+ * NOTE: assumes a single ProteinView. Unlike the genome-highlight bridge (which
+ * pairs by the declared `connectedViewId`, see getStructuresConnectedTo), a
+ * second ProteinView's MSA hover sync is skipped — pairing an MSA to one of
+ * several protein views has no reliable rule when the protein view declares
+ * neither a connectedMsaViewId nor a connectedViewId.
+ */
+export declare function getProteinView(session: AbstractSessionModel): HighlightSourceProteinView | undefined;
+interface ConnectableStructure {
+    connectedViewId?: string;
+}
+/**
+ * Every structure across all ProteinViews that declares this genome view as its
+ * connection. Structures are paired to a genome view explicitly, so a second
+ * LinearGenomeView doesn't mirror another view's highlights (the coordinates
+ * would be meaningless there, possibly on a different assembly), and a second
+ * ProteinView isn't ignored.
+ */
+export declare function getStructuresConnectedTo<T extends ConnectableStructure>(proteinViews: {
+    structures: T[];
+}[], viewId: string): T[];
+export {};

package/dist/AddHighlightModel/proteinViewLookup.js

@@ -0,0 +1,23 @@
+export function getProteinViews(session) {
+    return session.views.filter(v => v.type === 'ProteinView');
+}
+/**
+ * NOTE: assumes a single ProteinView. Unlike the genome-highlight bridge (which
+ * pairs by the declared `connectedViewId`, see getStructuresConnectedTo), a
+ * second ProteinView's MSA hover sync is skipped — pairing an MSA to one of
+ * several protein views has no reliable rule when the protein view declares
+ * neither a connectedMsaViewId nor a connectedViewId.
+ */
+export function getProteinView(session) {
+    return getProteinViews(session)[0];
+}
+/**
+ * Every structure across all ProteinViews that declares this genome view as its
+ * connection. Structures are paired to a genome view explicitly, so a second
+ * LinearGenomeView doesn't mirror another view's highlights (the coordinates
+ * would be meaningless there, possibly on a different assembly), and a second
+ * ProteinView isn't ignored.
+ */
+export function getStructuresConnectedTo(proteinViews, viewId) {
+    return proteinViews.flatMap(view => view.structures.filter(s => s.connectedViewId === viewId));
+}

package/dist/AddHighlightModel/util.d.ts

@@ -1,5 +1,3 @@
-import type { JBrowsePluginProteinViewModel } from '../ProteinView/model';
-import type { AbstractSessionModel } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export interface HighlightRegion {
     refName: string;
@@ -20,4 +18,3 @@ export declare const useStyles: (params: void, muiStyleOverridesParams?: {
     css: import("tss-react").Css;
     cx: import("tss-react").Cx;
 };
-export declare function getProteinView(session: AbstractSessionModel): JBrowsePluginProteinViewModel | undefined;

package/dist/AddHighlightModel/util.js

@@ -34,7 +34,3 @@ export const useStyles = makeStyles()({
         border: '1px solid black',
     },
 });
-export function getProteinView(session) {
-    const view = session.views.find(v => v.type === 'ProteinView');
-    return view;
-}

package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js

@@ -43,7 +43,9 @@ const AlphaFoldDBSearch = observer(function AlphaFoldDBSearch({ feature, session
             state.error ? React.createElement(ErrorMessage, { error: state.error }) : null,
             React.createElement(UniProtIdInput, { lookupMode: state.lookupMode, onLookupModeChange: state.setLookupMode, manualUniprotId: state.manualUniprotId, onManualUniprotIdChange: state.setManualUniprotId, featureUniprotId: state.featureUniprotId, hasProteinSequence: !!state.userSelectedProteinSequence?.seq, sequenceSearchType: state.sequenceSearchType, onSequenceSearchTypeChange: state.setSequenceSearchType, endContent: state.showIdentifierSelector ? (React.createElement("div", { className: classes.endRow },
                     React.createElement(IdentifierSelector, { recognizedIds: state.recognizedIds, geneName: state.geneName, selectedId: state.selectedQueryId, onSelectedIdChange: state.setSelectedQueryId }),
-                    React.createElement(TextField, { size: "small", label: "Organism (NCBI taxon)", helperText: "Scopes the gene-name search", value: state.taxonId, onChange: event => { state.setTaxonId(event.target.value); }, placeholder: String(state.effectiveTaxonId), slotProps: { inputLabel: { shrink: true } }, sx: { width: 180 } }))) : null }),
+                    React.createElement(TextField, { size: "small", label: "Organism (NCBI taxon)", helperText: "Scopes the gene-name search", value: state.taxonId, onChange: event => {
+                            state.setTaxonId(event.target.value);
+                        }, placeholder: String(state.effectiveTaxonId), slotProps: { inputLabel: { shrink: true } }, sx: { width: 180 } }))) : null }),
             state.loadingStatuses.map(status => (React.createElement(LoadingEllipses, { key: status, variant: "subtitle2", message: status }))),
             state.showUniprotResults && (React.createElement(React.Fragment, null,
                 React.createElement(Typography, { variant: "body2", color: "textSecondary" },

package/dist/LaunchProteinView/components/AlphaFoldDBSearchStatus.js

@@ -2,6 +2,7 @@ import React from 'react';
 import { Typography } from '@mui/material';
 import IsoformSequencesToggle from './IsoformSequencesToggle';
 import ExternalLink from '../../components/ExternalLink';
+import { uniprotEntryUrl } from '../utils/structureUrls';
 import { getTranscriptDisplayName } from '../utils/util';
 function NotFound({ uniprotId }) {
     return (React.createElement(Typography, null,
@@ -15,7 +16,7 @@ export default function AlphaFoldDBSearchStatus({ uniprotId, selectedTranscript,
             React.createElement(Typography, null,
                 "UniProt link:",
                 ' ',
-                React.createElement(ExternalLink, { href: `https://www.uniprot.org/uniprotkb/${uniprotId}/entry` }, uniprotId)),
+                React.createElement(ExternalLink, { href: uniprotEntryUrl(uniprotId) }, uniprotId)),
             React.createElement(Typography, null,
                 "AlphaFoldDB link: ",
                 React.createElement(ExternalLink, { href: url }, url))),

package/dist/LaunchProteinView/components/FoldseekActionMenu.js

@@ -3,7 +3,8 @@ import { ErrorMessage } from '@jbrowse/core/ui';
 import { Button, Menu, MenuItem } from '@mui/material';
 import { useSafeLaunch } from '../hooks/useSafeLaunch';
 import { caCoordsToPdb, hasValidCaCoords } from '../utils/caCoordsToPdb';
-import { getConditionalProteinLaunches, getConfidenceUrlFromTarget, getUniprotIdFromAlphaFoldTarget, launch3DProteinView, } from '../utils/launchViewUtils';
+import { getConditionalProteinLaunches, launch3DProteinView, } from '../utils/launchViewUtils';
+import { getConfidenceUrlFromTarget, getUniprotIdFromAlphaFoldTarget, } from '../utils/structureUrls';
 export default function FoldseekActionMenu({ hit, session, view, feature, selectedTranscript, userProvidedTranscriptSequence, onClose, }) {
     const [anchorEl, setAnchorEl] = useState(null);
     const open = Boolean(anchorEl);
@@ -18,7 +19,7 @@ export default function FoldseekActionMenu({ hit, session, view, feature, select
     const baseParams = { session, view, feature, selectedTranscript, uniprotId };
     const handleLaunch3D = runLaunch(() => {
         // Use tCa coordinates to generate PDB data if no URL is available
-        const pdbData = !hit.structureUrl && hasValidCaCoords(hit.tCa, hit.tSeq)
+        const pdbData = !hit.structureUrl && hasValidCaCoords(hit)
             ? caCoordsToPdb(hit.tCa, hit.tSeq, 'A', hit.target)
             : undefined;
         launch3DProteinView({
@@ -32,7 +33,7 @@ export default function FoldseekActionMenu({ hit, session, view, feature, select
         ...baseParams,
         confidenceUrl: getConfidenceUrlFromTarget(hit.target),
     });
-    const canLoad = !!hit.structureUrl || hasValidCaCoords(hit.tCa, hit.tSeq);
+    const canLoad = !!hit.structureUrl || hasValidCaCoords(hit);
     if (!canLoad) {
         return React.createElement("span", null, "-");
     }

package/dist/LaunchProteinView/components/FoldseekResultsTable.js

@@ -2,7 +2,7 @@ import React from 'react';
 import { Paper, Table, TableBody, TableCell, TableContainer, TableHead, TableRow, Typography, } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 import FoldseekActionMenu from './FoldseekActionMenu';
-import { getStructureUrlFromTarget } from '../utils/launchViewUtils';
+import { getStructureUrlFromTarget } from '../utils/structureUrls';
 const useStyles = makeStyles()(theme => ({
     root: {
         display: 'flex',

package/dist/LaunchProteinView/components/FoldseekSearch.js

@@ -9,7 +9,7 @@ import TranscriptSelector from './TranscriptSelector';
 import useFoldseekSearch from '../hooks/useFoldseekSearch';
 import useTranscriptIsoformSelection from '../hooks/useTranscriptIsoformSelection';
 import { DEFAULT_DATABASES } from '../services/foldseekApi';
-import { stripStopCodon } from '../utils/util';
+import { stripAllStopCodons } from '../utils/util';
 const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
@@ -33,7 +33,7 @@ const FoldseekSearch = observer(function FoldseekSearch({ feature, session, view
     const { results, cleanedAaSequence, di3Sequence, isLoading, isPredicting, error, statusMessage, predictStructure, search, reset, } = useFoldseekSearch();
     const { transcripts, isoformSequences, isLoading: isLoadingIsoforms, error: isoformError, selectedTranscriptId: effectiveSelectedTranscriptId, setSelectedTranscriptId: setUserSelection, selectedTranscript, selectedIsoform: selectedIsoformData, } = useTranscriptIsoformSelection({ feature, view });
     const cleanedSequence = selectedIsoformData
-        ? stripStopCodon(selectedIsoformData.seq)
+        ? stripAllStopCodons(selectedIsoformData.seq)
         : '';
     const sequence = userEditedSequence ?? cleanedSequence;
     // Any change to the input sequence makes an existing 3Di prediction (and any

package/dist/LaunchProteinView/components/LaunchProteinViewDialog.js

@@ -14,7 +14,7 @@ export default function LaunchProteinViewDialog({ handleClose, feature, model, }
     const [alignmentAlgorithm, setAlignmentAlgorithm] = useLocalStorage('jbrowse-protein3d-alignment-algorithm', DEFAULT_ALIGNMENT_ALGORITHM);
     const session = getSession(model);
     const view = getContainingView(model);
-    return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch protein view", titleNode: React.createElement(React.Fragment, null,
+    return (React.createElement(Dialog, { "data-testid": "launch-protein-view-dialog", maxWidth: "xl", title: "Launch protein view", titleNode: React.createElement(React.Fragment, null,
             "Launch protein view ",
             React.createElement(HelpButton, null)), open: true, onClose: handleClose },
         React.createElement(Tabs, { value: choice, onChange: (_, val) => {

package/dist/LaunchProteinView/components/ProteinViewActions.js

@@ -2,7 +2,7 @@ import React, { useState } from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
 import ArrowDropDownIcon from '@mui/icons-material/ArrowDropDown';
 import SettingsIcon from '@mui/icons-material/Settings';
-import { Button, ButtonGroup, IconButton, Tooltip, Typography } from '@mui/material';
+import { Button, ButtonGroup, IconButton, Tooltip, Typography, } from '@mui/material';
 import LaunchOptionsDialog from './LaunchOptionsDialog';
 import LaunchSettingsDialog from './LaunchSettingsDialog';
 import SequenceMismatchNotice from './SequenceMismatchNotice';
@@ -95,8 +95,8 @@ export default function ProteinViewActions({ handleClose, uniprotId, userSelecte
             } }, "Cancel"),
         showMissingReasons ? (React.createElement(Typography, { variant: "body2", color: "error", sx: { mr: 2 } }, missingReasons.join('. '))) : null,
         React.createElement(ButtonGroup, { variant: "contained", color: "primary", size: "small" },
-            React.createElement(Button, { disabled: !canLaunch, onClick: handleLaunch3DView }, "Launch"),
-            React.createElement(Button, { disabled: !canLaunch, onClick: () => {
+            React.createElement(Button, { "data-testid": "protein-launch-button", disabled: !canLaunch, onClick: handleLaunch3DView }, "Launch"),
+            React.createElement(Button, { "data-testid": "protein-launch-options-button", disabled: !canLaunch, onClick: () => {
                     setDialogOpen(true);
                 }, "aria-label": "More launch options" },
                 React.createElement(ArrowDropDownIcon, null))),

package/dist/LaunchProteinView/components/SequenceMismatchNotice.js

@@ -6,8 +6,7 @@ export default function SequenceMismatchNotice({ alignmentAlgorithm, onAlignment
     return (React.createElement(Typography, { variant: "body2", sx: { mr: 2, display: 'flex', alignItems: 'center' } },
         "Transcript and structure sequences differ, will run",
         ' ',
-        ALIGNMENT_ALGORITHM_LABELS[alignmentAlgorithm] ?? alignmentAlgorithm,
-        ' ',
-        "alignment",
+        ALIGNMENT_ALGORITHM_LABELS[alignmentAlgorithm],
+        " alignment",
         React.createElement(AlignmentSettingsButton, { value: alignmentAlgorithm, onChange: onAlignmentAlgorithmChange })));
 }

package/dist/LaunchProteinView/components/StructureSourcePicker.js

@@ -1,7 +1,7 @@
 import React from 'react';
 import { Button, FormControl, FormControlLabel, Radio, RadioGroup, TextField, Typography, } from '@mui/material';
 import HelpButton from './HelpButton';
-import { getPdbStructureUrl } from '../utils/launchViewUtils';
+import { getPdbStructureUrl } from '../utils/structureUrls';
 export default function StructureSourcePicker({ choice, setChoice, structureURL, setStructureURL, setFile, pdbId, setPdbId, }) {
     return (React.createElement("div", { style: { display: 'flex', margin: 30 } },
         React.createElement(Typography, null,

package/dist/LaunchProteinView/components/UniProtResultsTable.js

@@ -2,6 +2,7 @@ import React from 'react';
 import { Chip, Paper, Radio, Table, TableBody, TableCell, TableContainer, TableHead, TableRow, Typography, } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 import ExternalLink from '../../components/ExternalLink';
+import { uniprotEntryUrl } from '../utils/structureUrls';
 const useStyles = makeStyles()(theme => ({
     tableContainer: {
         maxHeight: 200,
@@ -57,7 +58,7 @@ export default function UniProtResultsTable({ entries, selectedAccession, onSele
                     React.createElement(TableCell, { padding: "checkbox" },
                         React.createElement(Radio, { checked: selectedAccession === entry.accession, size: "small" })),
                     React.createElement(TableCell, null,
-                        React.createElement(ExternalLink, { href: `https://www.uniprot.org/uniprotkb/${entry.accession}` }, entry.accession)),
+                        React.createElement(ExternalLink, { href: uniprotEntryUrl(entry.accession) }, entry.accession)),
                     React.createElement(TableCell, null, entry.geneName ?? '-'),
                     React.createElement(TableCell, null, entry.organismName ?? '-'),
                     React.createElement(TableCell, null, entry.proteinName

package/dist/LaunchProteinView/components/UserProvidedStructure.js

@@ -40,8 +40,10 @@ const UserProvidedStructure = observer(function UserProvidedStructure({ feature,
     const activeURL = choice === 'file' ? '' : structureURL;
     const { sequences: structureSequences, error: fileError } = useStructureFileSequence({ file: activeFile, url: activeURL });
     const structureName = activeFile?.name ?? activeURL.slice(activeURL.lastIndexOf('/') + 1);
-    const structureSequence = structureSequences?.[0];
-    const { transcripts: options, isoformSequences, selectedTranscriptId: userSelection, setSelectedTranscriptId: setUserSelection, selectedTranscript, selectedIsoform: protein, error: isoformError, } = useTranscriptIsoformSelection({ feature, view, structureSequence });
+    const { transcripts: options, isoformSequences, 
+    // the chain the isoforms are compared against — not blindly chain 0, which
+    // mismatched every heteromer the view itself went on to map correctly
+    structureSequence, selectedTranscriptId: userSelection, setSelectedTranscriptId: setUserSelection, selectedTranscript, selectedIsoform: protein, error: isoformError, } = useTranscriptIsoformSelection({ feature, view, structureSequences });
     const error = isoformError ?? launchError ?? fileError;
     const canLaunch = !!(activeURL || activeFile) && !!protein && !!selectedTranscript;
     const sequencesDiffer = !!protein?.seq &&

package/dist/LaunchProteinView/components/proteinAssemblySetup.js

@@ -1,3 +1,4 @@
+import { uniprotFastaUrl } from '../utils/structureUrls';
 /**
  * Sets up a temporary assembly for a protein sequence from UniProt
  */
@@ -12,7 +13,7 @@ export function setupProteinAssembly(session, uniprotId) {
                 type: 'UnindexedFastaAdapter',
                 rewriteRefNames: "jexl:split(refName,'|')[1]",
                 fastaLocation: {
-                    uri: `https://rest.uniprot.org/uniprotkb/${uniprotId}.fasta`,
+                    uri: uniprotFastaUrl(uniprotId),
                 },
             },
         },

package/dist/LaunchProteinView/components/proteinTrackSetup.d.ts

@@ -1,45 +1,4 @@
 import type { SessionWithAddTracks } from '@jbrowse/core/util';
-/**
- * Fetches UniProt GFF data and extracts unique feature types
- */
-export declare function fetchUniProtFeatureTypes(uniprotId: string): Promise<string[]>;
-/**
- * Adds UniProt feature tracks for each feature type
- */
-export declare function addUniProtFeatureTracks({ session, uniprotId, featureTypes, }: {
-    session: SessionWithAddTracks;
-    uniprotId: string;
-    featureTypes: string[];
-}): void;
-/**
- * Adds antigen annotation track from EBI
- */
-export declare function addAntigenTrack({ session, uniprotId, }: {
-    session: SessionWithAddTracks;
-    uniprotId: string;
-}): void;
-/**
- * Adds variation track from EBI
- */
-export declare function addVariationTrack({ session, uniprotId, }: {
-    session: SessionWithAddTracks;
-    uniprotId: string;
-}): void;
-/**
- * Adds AlphaFold confidence track
- */
-export declare function addAlphaFoldConfidenceTrack({ session, uniprotId, confidenceUrl, }: {
-    session: SessionWithAddTracks;
-    uniprotId: string;
-    confidenceUrl: string | undefined;
-}): void;
-/**
- * Adds AlphaMissense pathogenicity scores track
- */
-export declare function addAlphaMissenseTrack({ session, uniprotId, }: {
-    session: SessionWithAddTracks;
-    uniprotId: string;
-}): void;
 /**
  * Adds all protein annotation tracks for a given UniProt ID
  */

package/dist/LaunchProteinView/components/proteinTrackSetup.js

@@ -1,26 +1,24 @@
+import { myfetch } from '../../fetchUtils';
+import { uniprotGffUrl } from '../utils/structureUrls';
 /**
  * Fetches UniProt GFF data and extracts unique feature types
  */
-export async function fetchUniProtFeatureTypes(uniprotId) {
-    const url = `https://rest.uniprot.org/uniprotkb/${uniprotId}.gff`;
-    const res = await fetch(url);
-    if (!res.ok) {
-        throw new Error(`HTTP ${res.status} fetching ${url}`);
-    }
-    const data = await res.text();
+async function fetchUniProtFeatureTypes(uniprotId) {
+    const data = await (await myfetch(uniprotGffUrl(uniprotId))).text();
     return [
         ...new Set(data
             .split('\n')
             .filter(f => !f.startsWith('#'))
-            .map(f => f.trim())
-            .filter(f => !!f)
-            .map(f => f.split('\t')[2])),
+            // column 3 is the GFF type; a line without one would otherwise become an
+            // `undefined`-named track
+            .map(f => f.split('\t')[2]?.trim())
+            .filter((f) => !!f)),
     ];
 }
 /**
  * Adds UniProt feature tracks for each feature type
  */
-export function addUniProtFeatureTracks({ session, uniprotId, featureTypes, }) {
+function addUniProtFeatureTracks({ session, uniprotId, featureTypes, }) {
     featureTypes.forEach(type => {
         const trackId = `${uniprotId}-${type}`;
         session.addTrackConf({
@@ -30,7 +28,7 @@ export function addUniProtFeatureTracks({ session, uniprotId, featureTypes, }) {
             adapter: {
                 type: 'Gff3Adapter',
                 gffLocation: {
-                    uri: `https://rest.uniprot.org/uniprotkb/${uniprotId}.gff`,
+                    uri: uniprotGffUrl(uniprotId),
                 },
             },
             assemblyNames: [uniprotId],
@@ -47,7 +45,7 @@ export function addUniProtFeatureTracks({ session, uniprotId, featureTypes, }) {
 /**
  * Adds antigen annotation track from EBI
  */
-export function addAntigenTrack({ session, uniprotId, }) {
+function addAntigenTrack({ session, uniprotId, }) {
     session.addTrackConf({
         type: 'FeatureTrack',
         trackId: `${uniprotId}-Antigen`,
@@ -64,7 +62,7 @@ export function addAntigenTrack({ session, uniprotId, }) {
 /**
  * Adds variation track from EBI
  */
-export function addVariationTrack({ session, uniprotId, }) {
+function addVariationTrack({ session, uniprotId, }) {
     session.addTrackConf({
         type: 'FeatureTrack',
         trackId: `${uniprotId}-Variation`,
@@ -81,7 +79,7 @@ export function addVariationTrack({ session, uniprotId, }) {
 /**
  * Adds AlphaFold confidence track
  */
-export function addAlphaFoldConfidenceTrack({ session, uniprotId, confidenceUrl, }) {
+function addAlphaFoldConfidenceTrack({ session, uniprotId, confidenceUrl, }) {
     if (confidenceUrl) {
         session.addTrackConf({
             type: 'QuantitativeTrack',
@@ -100,7 +98,7 @@ export function addAlphaFoldConfidenceTrack({ session, uniprotId, confidenceUrl,
 /**
  * Adds AlphaMissense pathogenicity scores track
  */
-export function addAlphaMissenseTrack({ session, uniprotId, }) {
+function addAlphaMissenseTrack({ session, uniprotId, }) {
     session.addTrackConf({
         type: 'MultiQuantitativeTrack',
         trackId: `${uniprotId}-AlphaMissense-scores`,

package/dist/LaunchProteinView/hooks/useAlphaFoldDBSearch.js

@@ -26,7 +26,9 @@ export default function useAlphaFoldDBSearch({ feature, view, }) {
         ? extractTaxonId(getConf(assembly, ['sequence', 'metadata']))
         : undefined;
     const overrideTaxon = Number(taxonIdInput.trim());
-    const effectiveTaxonId = taxonIdInput.trim() !== '' && Number.isFinite(overrideTaxon) && overrideTaxon > 0
+    const effectiveTaxonId = taxonIdInput.trim() !== '' &&
+        Number.isFinite(overrideTaxon) &&
+        overrideTaxon > 0
         ? overrideTaxon
         : assemblyTaxonId;
     const [selectedQueryId, setSelectedQueryId] = useState('auto');
@@ -55,13 +57,13 @@ export default function useAlphaFoldDBSearch({ feature, view, }) {
             : effectiveLookupMode === 'manual'
                 ? debouncedManualUniprotId
                 : undefined;
-    const { isLoading: isAlphaFoldLoading, isValidating: isAlphaFoldValidating, error: alphaFoldError, url: alphaFoldUrl, confidenceUrl: alphaFoldConfidenceUrl, structureSequence: alphaFoldStructureSequence, } = useAlphaFoldData({
+    const { isLoading: isAlphaFoldLoading, isValidating: isAlphaFoldValidating, error: alphaFoldError, url: alphaFoldUrl, confidenceUrl: alphaFoldConfidenceUrl, structureSequences: alphaFoldStructureSequences, } = useAlphaFoldData({
         uniprotId: isSequenceMode ? undefined : uniprotId,
     });
-    const { transcripts: transcriptOptions, isoformSequences, isLoading: isIsoformLoading, error: isoformError, selectedTranscriptId: effectiveTranscriptId, setSelectedTranscriptId: setUserSelection, selectedTranscript, selectedIsoform: userSelectedProteinSequence, } = useTranscriptIsoformSelection({
+    const { transcripts: transcriptOptions, isoformSequences, structureSequence: alphaFoldStructureSequence, isLoading: isIsoformLoading, error: isoformError, selectedTranscriptId: effectiveTranscriptId, setSelectedTranscriptId: setUserSelection, selectedTranscript, selectedIsoform: userSelectedProteinSequence, } = useTranscriptIsoformSelection({
         feature,
         view,
-        structureSequence: alphaFoldStructureSequence,
+        structureSequences: alphaFoldStructureSequences,
         resetKey: uniprotId,
     });
     const { uniprotId: seqSearchUniprotId, cifUrl: seqSearchUrl, plddtDocUrl: seqSearchConfidenceUrl, structureSequence: seqSearchStructureSequence, isLoading: isSequenceSearchLoading, isValidating: isSequenceSearchValidating, error: sequenceSearchError, } = useAlphaFoldSequenceSearch({

package/dist/LaunchProteinView/hooks/useAlphaFoldData.d.ts

@@ -6,5 +6,5 @@ export default function useAlphaFoldData({ uniprotId, }: {
     error: any;
     url: string | undefined;
     confidenceUrl: string | undefined;
-    structureSequence: string | undefined;
+    structureSequences: string[] | undefined;
 };

package/dist/LaunchProteinView/hooks/useAlphaFoldData.js

@@ -1,5 +1,5 @@
 import useStructureFileSequence from './useStructureFileSequence';
-import { getAlphaFoldConfidenceUrl, getAlphaFoldStructureUrl, } from '../utils/launchViewUtils';
+import { getAlphaFoldConfidenceUrl, getAlphaFoldStructureUrl, } from '../utils/structureUrls';
 export default function useAlphaFoldData({ uniprotId, }) {
     const url = uniprotId ? getAlphaFoldStructureUrl(uniprotId) : undefined;
     const confidenceUrl = uniprotId
@@ -12,6 +12,6 @@ export default function useAlphaFoldData({ uniprotId, }) {
         error,
         url,
         confidenceUrl,
-        structureSequence: sequences?.[0],
+        structureSequences: sequences,
     };
 }

package/dist/LaunchProteinView/hooks/useAlphaFoldSequenceSearch.js

@@ -3,13 +3,13 @@ import useSWR from 'swr';
 import { STATIC_SWR_OPTIONS } from './swrOptions';
 import { jsonfetch } from '../../fetchUtils';
 import { md5 } from '../utils/md5';
-import { stripStopCodon } from '../utils/util';
+import { stripAllStopCodons } from '../utils/util';
 export default function useAlphaFoldSequenceSearch({ sequence, searchType, enabled = true, }) {
     const searchValue = useMemo(() => {
         if (!sequence) {
             return undefined;
         }
-        const cleanSeq = stripStopCodon(sequence.toUpperCase());
+        const cleanSeq = stripAllStopCodons(sequence.toUpperCase());
         return searchType === 'md5' ? md5(cleanSeq) : cleanSeq;
     }, [sequence, searchType]);
     const { data, error, isLoading, isValidating } = useSWR(enabled && searchValue

package/dist/LaunchProteinView/hooks/useStructureFileSequence.js

@@ -4,22 +4,13 @@ import { addStructureFromData } from '../../ProteinView/addStructureFromData';
 import { addStructureFromURL } from '../../ProteinView/addStructureFromURL';
 import { extractStructureSequences } from '../../ProteinView/extractStructureSequences';
 import { withTemporaryMolstarPlugin } from '../../ProteinView/withTemporaryMolstarPlugin';
-function detectStructureFormat(fileName) {
-    const dot = fileName.lastIndexOf('.');
-    const ext = dot >= 0 ? fileName.slice(dot + 1).toLowerCase() : '';
-    if (ext === 'cif' || ext === 'mmcif' || ext === 'bcif') {
-        return 'mmcif';
-    }
-    return 'pdb';
-}
+// Format is detected by addStructureFromData/addStructureFromURL themselves.
+// This hook used to detect it here, for the file branch only, which meant the
+// dialog preview and the view that followed could disagree about the same file.
 async function fetchSequences({ file, url }) {
     return withTemporaryMolstarPlugin(async (plugin) => {
         const { model } = file
-            ? await addStructureFromData({
-                data: await file.text(),
-                plugin,
-                format: detectStructureFormat(file.name),
-            })
+            ? await addStructureFromData({ data: await file.text(), plugin })
             : await addStructureFromURL({ url: url, plugin });
         return extractStructureSequences(model);
     });

package/dist/LaunchProteinView/hooks/useTranscriptIsoformSelection.d.ts

@@ -1,14 +1,15 @@
 import type { Feature } from '@jbrowse/core/util';
-export default function useTranscriptIsoformSelection({ feature, view, structureSequence, resetKey, }: {
+export default function useTranscriptIsoformSelection({ feature, view, structureSequences, resetKey, }: {
     feature: Feature;
     view?: {
         assemblyNames?: string[];
     };
-    structureSequence?: string;
+    structureSequences?: string[];
     resetKey?: string;
 }): {
     transcripts: Feature[];
     isoformSequences: import("../utils/util").IsoformSequences | undefined;
+    structureSequence: string | undefined;
     isLoading: boolean;
     error: any;
     selectedTranscriptId: string | undefined;

package/dist/LaunchProteinView/hooks/useTranscriptIsoformSelection.js

@@ -1,15 +1,17 @@
 import useIsoformProteinSequences from './useIsoformProteinSequences';
 import useTranscriptSelection from './useTranscriptSelection';
-import { getId, getTranscriptFeatures } from '../utils/util';
+import { getId, getTranscriptFeatures, pickStructureSequence, } from '../utils/util';
 // Bundles the transcript-isoform wiring shared by all three launch tabs:
-// list transcripts, fetch their protein sequences, auto/manually select one,
-// and resolve the selection back to its feature + sequence.
-export default function useTranscriptIsoformSelection({ feature, view, structureSequence, resetKey, }) {
+// list transcripts, fetch their protein sequences, pick which chain of the
+// structure to compare against, auto/manually select a transcript, and resolve
+// the selection back to its feature + sequence.
+export default function useTranscriptIsoformSelection({ feature, view, structureSequences, resetKey, }) {
     const transcripts = getTranscriptFeatures(feature);
     const { isoformSequences, isLoading, error } = useIsoformProteinSequences({
         feature,
         view,
     });
+    const structureSequence = pickStructureSequence(structureSequences, isoformSequences);
     const { userSelection, setUserSelection } = useTranscriptSelection({
         options: transcripts,
         isoformSequences,
@@ -23,6 +25,7 @@ export default function useTranscriptIsoformSelection({ feature, view, structure
     return {
         transcripts,
         isoformSequences,
+        structureSequence,
         isLoading,
         error,
         selectedTranscriptId: userSelection,